NeurIPS 2025 Papers

Conference on Neural Information Processing Systems

Decision breakdown

5,812papers

Counted from the official paper list; may differ slightly from the number the conference announced.

  • Oral
    931.6%
  • Spotlight
    73912.7%
  • Poster
    4,98085.7%

Browse all papers

Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models

Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, Ozlem Garibay

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The growing importance of mRNA therapeutics and synthetic biology highlights the need for models that capture the latent structure of synonymous codon (different triplets encoding the same amino acid) usage, which subtly modulates translation efficiency and gene expression. While recent efforts incorporate codon-level inductive biases through auxiliary objectives, they often fall short of explicitly modeling the structured relationships that arise from the genetic code’s inherent symmetries. We introduce Equi‑mRNA, the first codon‑level equivariant mRNA language model that explicitly encodes synonymous codon symmetries as cyclic subgroups of 2D Special Orthogonal matrix ($\mathrm{SO}(2)$). By combining group‑theoretic priors with an auxiliary equivariance loss and symmetry‑aware pooling, Equi‑mRNA learns biologically grounded representations that outperform vanilla baselines across multiple axes. On downstream property‑prediction tasks including expression, stability, and riboswitch switching Equi‑mRNA delivers up to $\approx$ 10\% improvements in accuracy. In sequence generation, it produces mRNA constructs that are up to $\approx$ 4$\times$ more realistic under Fréchet BioDistance metrics and $\approx$ 28\% better preserve functional properties compared to vanilla baseline. Interpretability analyses further reveal that learned codon‑rotation distributions recapitulate known GC‑content biases and tRNA abundance patterns, offering novel insights into codon usage. Equi‑mRNA establishes a new biologically principled paradigm for mRNA modeling, with significant implications for the design of next‑generation therapeutics.

Poster
TP-MDDN: Task-Preferenced Multi-Demand-Driven Navigation with Autonomous Decision-Making

Shanshan Li, Da Huang, Yu He, Yanwei Fu, Yu-Gang Jiang, Xiangyang Xue

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In daily life, people often move through spaces to find objects that meet their needs, posing a key challenge in embodied AI. Traditional Demand-Driven Navigation (DDN) handles one need at a time but does not reflect the complexity of real-world tasks involving multiple needs and personal choices. To bridge this gap, we introduce Task-Preferenced Multi-Demand-Driven Navigation (TP-MDDN), a new benchmark for long-horizon navigation involving multiple sub-demands with explicit task preferences. To solve TP-MDDN, we propose AWMSystem, an autonomous decision-making system composed of three key modules: BreakLLM (instruction decomposition), LocateLLM (goal selection), and StatusMLLM (task monitoring). For spatial memory, we design MASMap, which combines 3D point cloud accumulation with 2D semantic mapping for accurate and efficient environmental understanding. Our Dual-Tempo action generation framework integrates zero-shot planning with policy-based fine control, and is further supported by an Adaptive Error Corrector that handles failure cases in real time. Experiments demonstrate that our approach outperforms state-of-the-art baselines in both perception accuracy and navigation robustness.

Poster
Continuous Concepts Removal in Text-to-image Diffusion Models

Tingxu Han, Weisong Sun, Yanrong Hu, Chunrong Fang, Yonglong zhang, Shiqing Ma, Tao Zheng, Zhenyu Chen, Zhenting Wang

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Text-to-image diffusion models have shown an impressive ability to generate high-quality images from input textual descriptions/prompts. However, concerns have been raised about the potential for these models to create content that infringes on copyrights or depicts disturbing subject matter. Removing specific concepts from these models is a promising solution to this issue. However, existing methods for concept removal do not work well in practical but challenging scenarios where concepts need to be continuously removed. Specifically, these methods lead to poor alignment between the text prompts and the generated image after the continuous removal process. To address this issue, we propose a novel concept removal approach called CCRT that includes a designed knowledge distillation paradigm. CCRT constrains the text-image alignment behavior during the continuous concept removal process by using a set of text prompts. These prompts are generated through our genetic algorithm, which employs a designed fuzzing strategy. To evaluate the effectiveness of CCRT, we conduct extensive experiments involving the removal of various concepts, algorithmic metrics, and human studies. The results demonstrate that CCRT can effectively remove the targeted concepts from the model in a continuous manner while maintaining the high image generation quality (e.g., text-image alignment). The code of CCRT is available at https://github.com/wssun/CCRT.

Poster
Role Bias in Diffusion Models: Diagnosing and Mitigating through Intermediate Decomposition

Sina Malakouti, Adriana Kovashka

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Text-to-image (T2I) diffusion models exhibit impressive photorealistic image generation capabilities, yet they struggle in compositional image generation. In this work, we introduce RoleBench, a benchmark focused on evaluating compositional generalization in action-based relations (e.g., "mouse chasing cat"). We show that state-of-the-art T2I models and compositional generation methods consistently default to frequent reversed relations (i.e., "cat chasing mouse"), a phenomenon we call role collapse. Related works attribute this to the model’s architectural limitation or underrepresentation in the data. Our key insight reveals that while models fail on rare compositions when their inversions are common, they can successfully generate similar intermediate compositions (e.g., "mouse chasing boy"), suggesting that this limitation is also due to the presence of frequent counterparts rather than just the absence of rare compositions. Motivated by this, we hypothesize that directional decomposition can gradually mitigate role collapse. We test this via ReBind, a lightweight framework that teaches role bindings using carefully selected active/passive intermediate compositions. Experiments suggest that intermediate compositions through simple fine-tuning can significantly reduce role collapse, with humans preferring ReBind more than 78% compared to state-of-the-art methods. Our findings highlight the role of distributional asymmetries in compositional failures and offer a simple, effective path for improving generalization.

Poster
VAGEN: Reinforcing World Model Reasoning for Multi-Turn VLM Agents

Kangrui Wang, Pingyue Zhang, Zihan Wang, Yaning Gao, Linjie Li, Qineng Wang, Hanyang Chen, Yiping Lu, Zhengyuan Yang, Lijuan Wang, Ranjay Krishna, Jiajun Wu, Li Fei-Fei, Yejin Choi, Manling Li

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A major challenge in training VLM agents, compared to LLM agents, is that states shift from simple texts to complex visual observations, which introduces partial observability and demands robust world modeling. We ask: can VLM agents build internal world models through explicit visual state reasoning? In this work, we architecturally enforce and reward VLM agent’s reasoning process via reinforcement learning (RL), formulating the problem as a Partially Observable Markov Decision Process (POMDP). We demonstrate that structuring agent’s reasoning into StateEstimation (“what is the current state?”) and TransitionModeling (“what is next?”) is critical by studying five reasoning strategies. Investigating how agents should ground visual states and represent these internal beliefs, we reveal the optimal representations are task-dependent: Natural Language excels at capturing semantic relationships for general tasks, while Structured formats are essential for high-precision manipulation. These insights motivate our approach to reward shaping and credit assignment. We leverage a WorldModeling Reward to densely rewards the agent’s turn-by-turn state predictions, while our Bi-Level General Advantage Estimation (Bi-Level GAE) enables turn-aware credit assignment. Through such world model reasoning, we enable a 3B model to achieve performance of 0.82 on a set of five diverse agent tasks, nearly 3× improvement over its untrained counterpart (0.21) and surpassing proprietary reasoning models like GPT-5 (0.75), Gemini 2.5 Pro (0.67) and Claude 4.5 (0.62). All experiments are supported by our VAGEN framework, a scalable system for training and analyzing multi-turn VLM agents across diverse visual environments

Poster
Escaping Collapse: The Strength of Weak Data for Large Language Model Training

Kareem Amin, Sara Babakniya, Alex Bie, Weiwei Kong, Umar Syed, Sergei Vassilvitskii

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Synthetically-generated data plays an increasingly larger role in training large language models. However, while synthetic data has been found to be useful, studies have also shown that without proper curation it can cause LLM performance to plateau, or even "collapse", after many training iterations. In this paper, we formalize this question and develop a theoretical framework to investigate how much curation is needed in order to ensure that LLM performance continually improves. Our analysis is inspired by boosting, a classic machine learning technique that leverages a very weak learning algorithm to produce an arbitrarily good classifier. The approach we analyze subsumes many recently proposed methods for training LLMs on synthetic data, and thus our analysis sheds light on why they are successful, and also suggests opportunities for future improvement. We present experiments that validate our theory, and show that dynamically focusing labeling resources on the most challenging examples --- in much the same way that boosting focuses the efforts of the weak learner --- leads to improved performance.

Poster
A Differential and Pointwise Control Approach to Reinforcement Learning

Minh Phuong Nguyen, Chandrajit L. Bajaj

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Reinforcement learning (RL) in continuous state-action spaces remains challenging in scientific computing due to poor sample efficiency and lack of pathwise physical consistency. We introduce Differential Reinforcement Learning (Differential RL), a novel framework that reformulates RL from a continuous-time control perspective via a differential dual formulation. This induces a Hamiltonian structure that embeds physics priors and ensures consistent trajectories without requiring explicit constraints. To implement Differential RL, we develop Differential Policy Optimization (dfPO), a pointwise, stage-wise algorithm that refines local movement operators along the trajectory for improved sample efficiency and dynamic alignment. We establish pointwise convergence guarantees, a property not available in standard RL, and derive a competitive theoretical regret bound of $\mathcal{O}(K^{5/6})$. Empirically, dfPO outperforms standard RL baselines on representative scientific computing tasks, including surface modeling, grid control, and molecular dynamics, under low-data and physics-constrained conditions.

Poster
LoRA vs Full Fine-tuning: An Illusion of Equivalence

Reece S Shuttleworth, Jacob Andreas, Antonio Torralba, Pratyusha Sharma

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Fine-tuning is a crucial paradigm for adapting pre-trained large language models to downstream tasks. Recently, methods like Low-Rank Adaptation (LoRA) have been shown to effectively fine-tune LLMs with an extreme reduction in trainable parameters. But, \emph{are their learned solutions really equivalent?} We study how LoRA and full-finetuning change pre-trained models by analyzing the model's weight matrices through the lens of their spectral properties. We find that LoRA and full fine-tuning yield weight matrices whose singular value decompositions exhibit very different structure: weight matrices trained with LoRA have new, high-ranking singular vectors, which we call \emph{intruder dimensions}, while those trained with full fine-tuning do not. Further, we extend the finding that LoRA forgets less than full fine-tuning and find its forgetting is vastly localized to the intruder dimension -- by causally intervening on the intruder dimensions by changing their associated singular values post-fine-tuning, we show that they cause forgetting. Moreover, scaling them down significantly improves modeling of the pre-training distribution with a minimal drop in downstream task performance. Given this, we should expect accumulating intruder dimensions to be harmful and lead to more forgetting. This will be amplified during continual learning because of sequentially fine-tuning, and we show that LoRA models do accumulate intruder dimensions here tend to perform worse in this setting, emphasizing the practicality of our findings.

Poster
Lost in Latent Space: An Empirical Study of Latent Diffusion Models for Physics Emulation

François Rozet, Ruben Ohana, Michael McCabe, Gilles Louppe, Francois Lanusse, Shirley Ho

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The steep computational cost of diffusion models at inference hinders their use as fast physics emulators. In the context of image and video generation, this computational drawback has been addressed by generating in the latent space of an autoencoder instead of the pixel space. In this work, we investigate whether a similar strategy can be effectively applied to the emulation of dynamical systems and at what cost. We find that the accuracy of latent-space emulation is surprisingly robust to a wide range of compression rates (up to 1000x). We also show that diffusion-based emulators are consistently more accurate than non-generative counterparts and compensate for uncertainty in their predictions with greater diversity. Finally, we cover practical design choices, spanning from architectures to optimizers, that we found critical to train latent-space emulators.

Poster
Reasoning Is Not a Race: When Stopping Early Beats Going Deeper

Mohan Zhang, Jiaxuan Gao, Shusheng Xu, Yi Wu

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We study the use of Process Reward Models (PRMs) for guiding Long Chain-of-Thought (CoT) reasoning in large language models. Although PRMs deliver fine-grained feedback in standard tasks, PRM-guided beam search does not consistently outperform PRM-free approaches in long CoT reasoning. We trace this shortfall to a "step quality degradation''—the expected step quality shows concave behavior, yielding unimodal or monotonically declining trends. To counteract this, we propose Z-Score Guided Early Stopping (ZGES), which halts search at the detected quality peak using local PRM-reward z-scores. Across multiple math benchmarks and model scales, ZGES outperforms both standard PRM-guided beam search and the PRM-free methods. Ablation studies further highlight the advantages and robustness of ZGES’s adaptive stopping mechanism.

Poster
Position: AI Should Sense Better, Not Just Scale Bigger: Adaptive Sensing as a Paradigm Shift

Eunsu Baek, Keondo Park, Jeonggil Ko, Min-hwan Oh, Taesik Gong, Hyung-Sin Kim

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Current AI advances largely rely on scaling neural models and expanding training datasets to achieve generalization and robustness. Despite notable successes, this paradigm incurs significant environmental, economic, and ethical costs, limiting sustainability and equitable access. Inspired by biological sensory systems, where adaptation occurs dynamically at the input (e.g., adjusting pupil size, refocusing vision)—we advocate for adaptive sensing as a necessary and foundational shift. Adaptive sensing proactively modulates sensor parameters (e.g., exposure, sensitivity, multimodal configurations) at the input level, significantly mitigating covariate shifts and improving efficiency. Empirical evidence from recent studies demonstrates that adaptive sensing enables small models (e.g., EfficientNet-B0) to surpass substantially larger models (e.g., OpenCLIP-H) trained with significantly more data and compute. We (i) outline a roadmap for broadly integrating adaptive sensing into real-world applications spanning humanoid, healthcare, autonomous systems, agriculture, and environmental monitoring, (ii) critically assess technical and ethical integration challenges, and (iii) propose targeted research directions, such as standardized benchmarks, real-time adaptive algorithms, multimodal integration, and privacy-preserving methods. Collectively, these efforts aim to transition the AI community toward sustainable, robust, and equitable artificial intelligence systems.

Poster
Policy Compatible Skill Incremental Learning via Lazy Learning Interface

Daehee Lee, Dongsu Lee, TaeYoon Kwack, Wonje Choi, Honguk Woo

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Skill Incremental Learning (SIL) is the process by which an embodied agent expands and refines its skill set over time by leveraging experience gained through interaction with its environment or by the integration of additional data. SIL facilitates efficient acquisition of hierarchical policies grounded in reusable skills for downstream tasks. However, as the skill repertoire evolves, it can disrupt compatibility with existing skill-based policies, limiting their reusability and generalization. In this work, we propose SIL-C, a novel framework that ensures skill-policy compatibility, allowing improvements in incrementally learned skills to enhance the performance of downstream policies without requiring policy re-training or structural adaptation. SIL-C employs a bilateral lazy learning-based mapping technique to dynamically align the subtask space referenced by policies with the skill space decoded into agent behaviors. This enables each subtask, derived from the policy's decomposition of a complex task, to be executed by selecting an appropriate skill based on trajectory distribution similarity. We evaluate SIL-C across diverse SIL scenarios and demonstrate that it maintains compatibility between evolving skills and downstream policies while ensuring efficiency throughout the learning process.

Spotlight
ARMesh: Autoregressive Mesh Generation via Next-Level-of-Detail Prediction

Jiabao Lei, Kewei Shi, Zhihao Liang, Kui Jia

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Directly generating 3D meshes, the default representation for 3D shapes in the graphics industry, using auto-regressive (AR) models has become popular these days, thanks to their sharpness, compactness in the generated results, and ability to represent various types of surfaces. However, AR mesh generative models typically construct meshes face by face in lexicographic order, which does not effectively capture the underlying geometry in a manner consistent with human perception. Inspired by 2D models that progressively refine images, such as the prevailing next-scale prediction AR models, we propose generating meshes auto-regressively in a progressive coarse-to-fine manner. Specifically, we view mesh simplification algorithms, which gradually merge mesh faces to build simpler meshes, as a natural fine-to-coarse process. Therefore, we generalize meshes to simplicial complexes and develop a transformer-based AR model to approximate the reverse process of simplification in the order of level of detail, constructing meshes initially from a single point and gradually adding geometric details through local remeshing, where the topology is not predefined and is alterable. Our experiments show that this novel progressive mesh generation approach not only provides intuitive control over generation quality and time consumption by early stopping the auto-regressive process but also enables applications such as mesh refinement and editing.

Poster
FACT: Mitigating Inconsistent Hallucinations in LLMs via Fact-Driven Alternating Code-Text Training

Xinxin You, Qixin Sun, Chenwei Yan, Xiao Zhang, Chen Ning, Xiangling Fu, Si Liu, Guoping Hu, Shijin Wang, Ji Wu, Xien Liu

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Inconsistent hallucinations remain a major challenge for large language models (LLMs), undermining the accuracy and reliability of fact-based reasoning in real-world applications. Existing approaches often rely on task-specific training or adaptation, such as hand-crafted synthetic datasets for domain tasks or solutions mainly focused on numerical reasoning, thereby limiting generalizability to broader, unseen NLP tasks. Inspired by the structural rigor and logical consistency of programming languages, we observe that fact-based texts can be mapped to programming structures due to their inherent patterns. We further propose FACT, a novel Fact-driven Alternating Code-text Training framework that alternates between text-to-code and code-to-text prediction. FACT is the first task-agnostic paradigm that embeds code and natural language in a shared semantic space, thereby transferring the logical consistency of code to LLM outputs in NLP tasks. Experiments show that with only a small subset of Wiki-40B-en for training, FACT reduces inconsistent hallucinations by 2.7%–8.0% and improves overall performance by 2.5%–6.1% in three leading LLMs and four diverse datasets covering QA and summarization tasks. This framework offers a new perspective on addressing challenging hallucinations in LLMs, contributing to more reliable AI.

Poster
Shortcutting Pre-trained Flow Matching Diffusion Models is Almost Free Lunch

Xu Cai, Yang Wu, Qianli Chen, Haoran Wu, Lichuan Xiang, Hongkai Wen

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We present an ultra-efficient post-training method for shortcutting large-scale pre-trained flow matching diffusion models into efficient few-step samplers, enabled by novel velocity field self-distillation. While shortcutting in flow matching, originally introduced by shortcut models, offers flexible trajectory-skipping capabilities, it requires a specialized step-size embedding incompatible with existing models unless retraining from scratch—a process nearly as costly as pretraining itself. Our key contribution is thus imparting a more aggressive shortcut mechanism to standard flow matching models (e.g., Flux), leveraging a unique distillation principle that obviates the need for step-size embedding. Working on the velocity field rather than sample space and learning rapidly from self-guided distillation in an online manner, our approach trains efficiently, e.g., producing a 3-step Flux <1 A100 day. Beyond distillation, our method can be incorporated into the pretraining stage itself, yielding models that inherently learn efficient, few-step flows without compromising quality. This capability also enables, to our knowledge, the first few-shot distillation method (e.g., 10 text-image pairs) for dozen-billion-parameter diffusion models, delivering state-of-the-art performance at almost free cost.

Poster
Train to Defend: First Defense Against Cryptanalytic Neural Network Parameter Extraction Attacks

Ashley Kurian, Aydin Aysu

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Neural networks are valuable intellectual property due to the significant computational cost, expert labor, and proprietary data involved in their development. Consequently, protecting their parameters is critical not only for maintaining a competitive advantage but also for enhancing the model's security and privacy. Prior works have demonstrated the growing capability of cryptanalytic attacks to scale to deeper models. In this paper, we present the first defense mechanism against cryptanalytic parameter extraction attacks. Our key insight is to eliminate the neuron uniqueness necessary for these attacks to succeed. We achieve this by a novel, extraction-aware training method. Specifically, we augment the standard loss function with an additional regularization term that minimizes the distance between neuron weights within a layer. Therefore, the proposed defense has zero area-delay overhead during inference. We evaluate the effectiveness of our approach in mitigating extraction attacks while analyzing the model accuracy across different architectures and datasets. When re-trained with the same model architecture, the results show that our defense incurs a marginal accuracy change of less than 1\% with the modified loss function. Moreover, we present a theoretical framework to quantify the success probability of the attack. When tested comprehensively with prior attack settings, our defense demonstrated empirical success for sustained periods of extraction, whereas unprotected networks are extracted between 14 minutes to 4 hours.

Poster
Unifying Reconstruction and Density Estimation via Invertible Contraction Mapping in One-Class Classification

Xiaolei Wang, Tianhong Dai, Huihui Bai, Yao Zhao, Jimin XIAO

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Due to the difficulty in collecting all unexpected abnormal patterns, One-Class Classification (OCC) has become the most popular approach to anomaly detection (AD). Reconstruction-based AD method relies on the discrepancy between inputs and reconstructed results to identify unobserved anomalies. However, recent methods trained only on normal samples may generalize to certain abnormal inputs, leading to well-reconstructed anomalies and degraded performance. To address this, we constrain reconstructions to remain on the normal manifold using a novel AD framework based on contraction mapping. This mapping guarantees that any input converges to a fixed point through iterations of this mapping. Based on this property, training the contraction mapping using only normal data ensures that its fixed point lies within the normal manifold. As a result, abnormal inputs are iteratively transformed toward the normal manifold, increasing the reconstruction error. In addition, the inherent invertibility of contraction mapping enables flow-based density estimation, where a prior distribution learned from the previous reconstruction is used to estimate the input likelihood for anomaly detection, further improving the performance. Using both mechanisms, we propose a bidirectional structure with forward reconstruction and backward density estimation. Extensive experiments on tabular data, natural image, and industrial image data demonstrate the effectiveness of our method. The code is available at URD.

Poster
Robust Cross-modal Alignment Learning for Cross-Scene Spatial Reasoning and Grounding

Yanglin Feng, Hongyuan Zhu, Dezhong Peng, Xi Peng, Xiaomin Song, Peng Hu

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Grounding target objects in 3D environments via natural language is a fundamental capability for autonomous agents to successfully fulfill user requests. Almost all existing works typically assume that the target object lies within a known scene and focus solely on in-scene localization. In practice, however, agents often encounter unknown or previously visited environments and need to search across a large archive of scenes to ground the described object, thereby invalidating this assumption. To address this, we reveal a novel task called Cross-Scene Spatial Reasoning and Grounding (CSSRG), which aims to locate a described object anywhere across an entire collection of 3D scenes rather than predetermined scenes. Due to the difference from existing 3D visual grounding, CSSRG poses two challenges: the prohibitive cost of exhaustively traversing all scenes and more complex cross-modal spatial alignment. To address the challenges, we propose a Cross-Scene 3D Object Reasoning Framework (CoRe), which adopts a matching-then-grounding pipeline to reduce computational overhead. Specifically, CoRe consists of i) a Robust Text-Scene Aligning (RTSA) module that learns global scene representations for robust alignment between object descriptions and the corresponding 3D scenes, enabling efficient retrieval of candidate scenes; and ii) a Tailored Word-Object Associating (TWOA) module that establishes fine-grained alignment between words and target objects to filter out redundant context, supporting precise object-level reasoning and alignment. Additionally, to benchmark CSSRG, we construct a new CrossScene-RETR dataset and evaluation protocol tailored for cross-scene grounding. Extensive experiments across four multimodal datasets demonstrate that CoRe dramatically reduces computational overhead while showing superiority in both scene retrieval and object grounding.

Poster
World Models as Reference Trajectories for Rapid Motor Adaptation

Carlos Stein Brito, Daniel C McNamee

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Learned control policies often fail when deployed in real-world environments with changing dynamics. When system dynamics shift unexpectedly, performance degrades until models are retrained on new data. We introduce Reflexive World Models (RWM), a dual control framework that uses world model predictions as implicit reference trajectories for rapid adaptation. Our method separates the control problem into long-term reward maximization through reinforcement learning and robust motor execution through reward-free rapid control in latent space. This dual architecture achieves significantly faster adaptation with low online computational cost compared to model-based RL baselines, while maintaining near-optimal performance. The approach combines the benefits of flexible policy learning through reinforcement learning with rapid error correction capabilities, providing a theoretically grounded method for maintaining performance in high-dimensional continuous control tasks under varying dynamics.

Poster
Context-Aware Regularization with Markovian Integration for Attention-Based Nucleotide Analysis

Mohammadsaleh Refahi, Mahdi Abavisani, Bahrad A. Sokhansanj, James R. Brown, Gail Rosen

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Transformers have revolutionized nucleotide sequence analysis, yet capturing long‑range dependencies remains challenging. Recent studies show that autoregressive transformers often exhibit Markovian behavior by relying on fixed-length context windows for next-token prediction. However, standard self-attention mechanisms are computationally inefficient for long sequences due to their quadratic complexity and do not explicitly enforce global transition consistency. We introduce CARMANIA (Context-Aware Regularization with Markovian Integration for Attention-Based Nucleotide Analysis), a self-supervised pretraining framework that augments next-token (NT) prediction with a transition-matrix (TM) loss. The TM loss aligns predicted token transitions with empirically derived n-gram statistics from each input sequence, encouraging the model to capture higher-order dependencies beyond local context. This integration enables CARMANIA to learn organism-specific sequence structures that reflect both evolutionary constraints and functional organization. We evaluate CARMANIA across diverse genomic tasks, including regulatory element prediction, functional gene classification, taxonomic inference, antimicrobial resistance detection, and biosynthetic gene cluster classification. CARMANIA outperforms the previous best long-context model by at least 7\%, matches state-of-the-art on shorter sequences (exceeding prior results on 20/40 tasks while running $\sim$2.5$\times$ faster), and shows particularly strong improvements on enhancer and housekeeping gene classification tasks—including up to a 34\% absolute gain in Matthews correlation coefficient (MCC) for enhancer prediction. The TM loss boosts accuracy in 33 of 40 tasks, especially where local motifs or regulatory patterns drive prediction. This enables more effective modeling of sequence-dependent biological features while maintaining robustness across non-coding and low-signal regions. Code available at https://github.com/EESI/carmania.

Poster